MolNFT v1 · #97278 · protein
Extracellular metalloproteinase from aspergillus
4K90 · Extracellular metalloproteinase mep: “Extracellular metalloproteinase from aspergillus”. X-ray diffraction, 5 ligands (NAG, BMA, CA), 6 pockets (best druggability 0.58). MolNFT v1 #97278 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4K90
- Type
- protein
- Length
- 596 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular metalloproteinase mep
- EC
- 3.4.24.-
- UniProt
- P46075
- Ligands
- NAG, BMA, CA, ZN, BO3
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular metalloproteinase mep (EC 3.4.24.-) | protein | 389 | 36% helix, 13% strand | P46075 |
| B | Extracellular metalloproteinase mep (EC 3.4.24.-) | protein | 207 | 20% helix, 41% strand | P46075 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A, B
- BO3 · Boric acid · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- MLA · Malonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.58 | 0.81 | 29 | empty |
| 2 | 142 | 0.57 | 0.83 | 29 | empty |
| 3 | 220 | 0.53 | 0.77 | 46 | BO3 |
| 4 | 67 | 0.52 | 0.86 | 15 | MLA |
| 5 | 84 | 0.40 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2031 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P46075
- Elsewhere: RCSB PDB 4K90 · PDBe 4K90 · UniProt P46075
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